Update README.md

README.md

@@ -82,3 +82,72 @@ configs:
   - split: train
     path: targets/train-*
 ---
+
+# ChEMBL 36
+
+ChEMBL 36 converted to HuggingFace `datasets` format. Source data is from the [ChEMBL database](https://www.ebi.ac.uk/chembl/) (EMBL-EBI), a manually curated database of bioactive molecules with drug-like properties.
+
+## Dataset configs
+
+### `molecules`
+
+All compounds in ChEMBL with canonical SMILES representations.
+
+| Column | Type | Description |
+|---|---|---|
+| `chembl_id` | string | ChEMBL compound identifier |
+| `canonical_smiles` | string | Canonical SMILES representation |
+| `molecule_type` | string | Compound type (e.g. `Small molecule`) |
+
+### `targets`
+
+Protein targets with amino-acid sequences. Multi-component targets (protein complexes) produce one row per component.
+
+| Column | Type | Description |
+|---|---|---|
+| `target_chembl_id` | string | ChEMBL target identifier |
+| `pref_name` | string | Preferred target name |
+| `target_type` | string | Target type (e.g. `SINGLE PROTEIN`, `PROTEIN COMPLEX`) |
+| `organism` | string | Source organism (e.g. `Homo sapiens`) |
+| `tax_id` | int64 | NCBI taxonomy ID |
+| `accession` | string | UniProt accession |
+| `sequence` | string | Amino-acid sequence |
+
+### `molecule_target_pairs`
+
+Paired bioactivity records linking compounds to protein targets. Filtered to rows with non-null SMILES, sequence, and pChEMBL value.
+
+| Column | Type | Description |
+|---|---|---|
+| `chembl_id` | string | ChEMBL compound identifier |
+| `canonical_smiles` | string | Canonical SMILES representation |
+| `target_chembl_id` | string | ChEMBL target identifier |
+| `target_pref_name` | string | Preferred target name |
+| `organism` | string | Target organism |
+| `sequence` | string | Amino-acid sequence (`\|`-separated for multi-component targets) |
+| `standard_type` | string | Activity type (e.g. `IC50`, `Ki`, `Kd`) |
+| `standard_value` | float64 | Raw activity value |
+| `standard_units` | string | Units (e.g. `nM`) |
+| `standard_relation` | string | Measurement relation (`=`, `<`, `>`) |
+| `pchembl_value` | float64 | Standardized −log₁₀ activity value |
+| `assay_type` | string | Assay classification (e.g. `B` for binding) |
+
+## Usage
+
+```python
+from datasets import load_dataset
+
+molecules = load_dataset("lukaskim/chembl-36", "molecules")
+targets   = load_dataset("lukaskim/chembl-36", "targets")
+pairs     = load_dataset("lukaskim/chembl-36", "molecule_target_pairs")
+```
+
+## Source
+
+Built from the [ChEMBL 36 SQLite release](https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_36/) using [chembl-hf](https://github.com/lukasmki/ChEMBL-HF).
+
+## License
+
+ChEMBL data is released under [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/). If you use this dataset, please cite the ChEMBL publication:
+
+> Zdrazil B, et al. (2024). The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity complementary data resources. *Nucleic Acids Research*, 52(D1), D1180–D1192. https://doi.org/10.1093/nar/gkad1004